The Interactorium: Visualising proteins, complexes and interaction networks in a virtual 3‐D cell

Abstract

Here, we describe the Interactorium, a tool in which a Virtual Cell is used as the context for the seamless visualisation of the yeast protein interaction network, protein complexes and protein 3-D structures. The tool has been designed to display very complex networks of up to 40 000 proteins or 6000 multiprotein complexes and has a series of toolboxes and menus to allow real-time data manipulation and control the manner in which data are displayed. It incorporates new algorithms that reduce the complexity of the visualisation by the generation of putative new complexes from existing data and by the reduction of edges through the use of protein "twins" when they occur in multiple locations. Since the Interactorium permits multi-level viewing of the molecular biology of the cell, it is a considerable advance over existing approaches. We illustrate its use for Saccharomyces cerevisiae but note that it will also be useful for the analysis of data from simpler prokaryotes and higher eukaryotes, including humans. The Interactorium is available for download at http://www.interactorium.net.

Phosphorylation of Intrinsically Disordered Regions in Remorin Proteins

“…The potato remorin StREM1.3 was originally discovered as a plasma membrane associated protein, which is strongly phosphorylated upon treatment with polygalacturonic acid (Farmer et al, 1989). In A. thaliana differential phosphorylation of the group 1 remorins AtREM1.2 (At3g61260) and AtREM1.3 (At2g45820) is dependent on the presence of the NBS–LRR resistance protein RPM1 (Widjaja et al, 2009) and triggered upon perception of microbe-associated molecular pattern (MAMPs; Benschop et al, 2007), respectively. The predominant detection of phosphopeptides from group 1b remorins in proteomic screens certainly reflects the high abundance of these members in plant cells.…”

Complex search: aggregation, discovery, and synthesis

“…Exploratory search information visualization focuses on the visual representation of large data collections to help people understand and analyse data [68]. In graphbased representation this property can be implemented by graph clustering and 3D graph visualization [71]. In many cases 3D graphs can outperform 2D graphs [38].…”

Visualization of the interactome: What are we looking at?

“…The compartment can be a protein complex, an organelle or any subcellular localization. One tool that enables the investigator to navigate in between an overview and a detailed view of an interactome, and trigger on‐the‐fly protein data display on demand is the Interactorium []. The entire visualization resembles a video game application that provides smooth multi‐scale navigation, including fly‐through (zooming in and out) and fly‐over, throughout the network, and provides automatic centering on any selected protein.…”

“…Yeast DNA ‐binding protein Rap1 and its interaction partners in the nucleus, generated with the use of the Interactorium []. Protein nodes are represented by circles in bright red; those with structural data are highlighted by a small green cross next to their gene name.…”